Jill Abramson and ‘The Confidence Code': A case study

FORTUNE — Katty Kay and Claire Shipman should be proud of Jill Abramson. The authors of The Confidence Code, Kay and Shipman recently put out a call to action for women to advocate for themselves and their value in the workplace. If we take yesterday’s New Yorker article as fact, the former executive editor of the New York Times did just that when she asked for more pay after discovering her male predecessor earned more.

Yet Abramson was reportedly not applauded for her effort to stand up for herself and the value she brought to the Times. Instead, top executives at the paper perceived her request for more money as “pushy,” and sources say it was contributing factor to her getting edged out of the executive role. So while Kay and Shipman indicate in their book on the “science and art and self-assurance” that women’s fears of being reprimanded for asserting themselves are unfounded, Abramson’s alleged story highlights a different result.

The New York TimesNYT did not respond immediately to Fortune’s request for comment.

Women are four times less likely to initiate salary negotiations than men, studies have shown. When women do negotiate, they typically ask for 30% less money than men do. The fear of asking for more is one of the often-cited reasons for the gender wage gap that continues to exist — even between women and men who work in the same occupation. But what if the workplace isn’t ready for a bunch of confidence wielding women standing up for themselves and their value? As was the case with Abramson, what’s the point of confidence if the system she worked within didn’t support it?

Confidence aside, strong-willed women cannot succeed in the workplace without the support of an accepting culture. A young female staffer at the Times told Amanda Hess of Slate that “we don’t have a great culture of female solidarity at the Times,” while another said “there’s still very much an Old Boys’ Club atmosphere here.” Both anecdotes indicate that an insupportable culture may be partly responsible for Abramson’s controversial downfall.

Ken Favaro, a senior partner at consulting firm Strategy& and the author of a recent study on gender imbalance in the C-Suite, also pointed to a “cultural drag” between the growing percentage of women in the workplace and the stagnating percentage reaching the executive level.

“A lot of these companies were started at least 50 years ago when there were no women in the workforce, much less running companies,” Favaro said. “It takes a long time for work culture to change.”

New America Foundation CEO Anne-Marie Slaughter made a similar point in 2013 when she explained in the Atlantic why she believes women still can’t have it all. “I see much less of an ambition gap and much more of a workplace and society that isn’t allowing us to use the talent that is multiplied well beyond this room,” Slaughter told Fortune at last year’s Most Powerful Women Summit. In Slaughter’s view, the expectations of women in power must change before the gender gap has any hope of becoming more narrow.

Indeed, the verdict is still out on why exactly the first female executive editor of the New York Times is suddenly fleeing the post. But as Rebecca Traister of the New Republic points out, whatever the real story is, it’s likely not a pretty one. After two and half years leading the Times through arguably the most disruptive time in history for journalism, Abramson will not remain at the paper or assist in former managing editor Dean Baquet’s transition to the executive role. Whether or not gender played into her dismissal, reporting to date suggests a workplace culture at the Times that could learn to be more accepting of vocal leaders like Abramson.

UPDATE: Times Company chairman Arthur Sulzbeger Jr. issued a memo Thursday stating that “It is simply not true that Jill’s compensation was significantly less than her predecessors” and “comparisons between the pensions of different executive editors are difficult.”